RT Journal
A1 Tasse, Lena
A1 Bercovici, Juliette
A1 Pizzut-Serin, Sandra
A1 Robe, Patrick
A1 Tap, Julien
A1 Klopp, Christophe
A1 Cantarel, Brandi L.
A1 Coutinho, Pedro M.
A1 Henrissat, Bernard
A1 Leclerc, Marion
A1 Doré, Joël
A1 Monsan, Pierre
A1 Remaud-Simeon, Magali
A1 Potocki-Veronese, Gabrielle
T1 Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes
JF Genome Research 
JO Genome Research 
YR 2010 
FD November 01 
VO 20 
IS 11 
SP 1605 
OP 1612 
DO 10.1101/gr.108332.110 
UL http://genome.cshlp.org/content/20/11/1605.abstract 
AB The human gut microbiome is a complex ecosystem composed mainly of uncultured bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material in our diet that is not metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes). We describe a multi-step functionally based approach to guide the in-depth pyrosequencing of specific regions of the human gut metagenome encoding the CAZymes involved in dietary fiber breakdown. High-throughput functional screens were first applied to a library covering 5.4 × 109 bp of metagenomic DNA, allowing the isolation of 310 clones showing beta-glucanase, hemicellulase, galactanase, amylase, or pectinase activities. Based on the results of refined secondary screens, sequencing efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA, corresponding to 26 clones that were particularly efficient for the degradation of raw plant polysaccharides. Seventy-three CAZymes from 35 different families were discovered. This corresponds to a fivefold target-gene enrichment compared to random sequencing of the human gut metagenome. Thirty-three of these CAZy encoding genes are highly homologous to prevalent genes found in the gut microbiome of at least 20 individuals for whose metagenomic data are available. Moreover, 18 multigenic clusters encoding complementary enzyme activities for plant cell wall degradation were also identified. Gene taxonomic assignment is consistent with horizontal gene transfer events in dominant gut species and provides new insights into the human gut functional trophic chain.